# frozen_string_literal: true require 'spec_helper' describe Bolognese::Metadata, vcr: true do context "write metadata as schema_org" do it "journal article" do input = "10.7554/eLife.01567" subject = Bolognese::Metadata.new(input: input, from: "crossref") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.7554/elife.01567") expect(json["@type"]).to eq("ScholarlyArticle") expect(json["isPartOf"]).to eq("@type"=>"Periodical", "issn"=>"2050-084X") expect(json["periodical"]).to eq("@type"=>"Journal", "identifier"=>"2050-084X", "identifierType"=>"ISSN", "name"=>"eLife", "volume"=>"3") expect(json["citation"].length).to eq(26) expect(json["citation"].first).to eq("@id"=>"https://doi.org/10.1038/nature02100", "@type"=>"CreativeWork") expect(json["funder"]).to eq([{"name"=>"SystemsX", "@type"=>"Organization"}, {"name"=>"EMBO", "@type"=>"Organization", "@id"=>"https://doi.org/10.13039/501100003043"}, {"name"=>"Swiss National Science Foundation", "@type"=>"Organization", "@id"=>"https://doi.org/10.13039/501100001711"}, {"name"=>"University of Lausanne", "@type"=>"Organization", "@id"=>"https://doi.org/10.13039/501100006390"}]) expect(json["license"]).to eq("https://creativecommons.org/licenses/by/3.0/legalcode") end it "maremma schema.org JSON" do input = "https://github.com/datacite/maremma" subject = Bolognese::Metadata.new(input: input, from: "codemeta") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5438/qeg0-3gm3") expect(json["@type"]).to eq("SoftwareSourceCode") expect(json["name"]).to eq("Maremma: a Ruby library for simplified network calls") expect(json["author"]).to eq("name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner", "@type"=>"Person", "@id"=>"https://orcid.org/0000-0003-0077-4738", "affiliation" => {"@type"=>"Organization", "name"=>"DataCite"}) end it "Schema.org JSON" do input = "https://doi.org/10.5281/ZENODO.48440" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5281/zenodo.48440") expect(json["@type"]).to eq("SoftwareSourceCode") expect(json["name"]).to eq("Analysis Tools For Crossover Experiment Of Ui Using Choice Architecture") expect(json["license"]).to eq(["https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode", "info:eu-repo/semantics/openAccess"]) end it "Schema.org JSON isReferencedBy" do input = "https://doi.org/10.5061/DRYAD.8515" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5061/dryad.8515") expect(json["@type"]).to eq("Dataset") expect(json["@reverse"]).to eq("citation" => [{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446", "@type"=>"ScholarlyArticle"}, {"@type"=>"ScholarlyArticle", "identifier"=>{"@type"=>"PropertyValue", "propertyID"=>"PMID", "value"=>"19478877"}}], "isBasedOn" => [{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446", "@type"=>"ScholarlyArticle"}, {"@type"=>"ScholarlyArticle", "identifier"=>{"@type"=>"PropertyValue", "propertyID"=>"PMID", "value"=>"19478877"}}]) expect(json["license"]).to eq("https://creativecommons.org/publicdomain/zero/1.0/legalcode") expect(json["keywords"]).to eq("Phylogeny, Malaria, Parasites, Taxonomy, Mitochondrial genome, Africa, Plasmodium") end it "Schema.org JSON IsSupplementTo" do input = "https://doi.org/10.5517/CC8H01S" subject = Bolognese::Metadata.new(input: input) json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5517/cc8h01s") expect(json["@type"]).to eq("Dataset") expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1107/s1600536804021154", "@type"=>"ScholarlyArticle"}) end it "Schema.org JSON Cyark" do input = "https://doi.org/10.26301/jgf3-jm06" subject = Bolognese::Metadata.new(input: input) json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.26301/jgf3-jm06") expect(json["@type"]).to eq("Dataset") end it "rdataone" do input = fixture_path + 'codemeta.json' subject = Bolognese::Metadata.new(input: input, from: "codemeta") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5063/f1m61h5x") expect(json["@type"]).to eq("SoftwareSourceCode") expect(json["name"]).to eq("R Interface to the DataONE REST API") expect(json["author"]).to eq([{"name"=>"Matt Jones", "givenName"=>"Matt", "familyName"=>"Jones", "@type"=>"Person", "@id"=>"https://orcid.org/0000-0003-0077-4738", "affiliation"=>{"@type"=>"Organization", "name"=>"NCEAS"}}, {"name"=>"Peter Slaughter", "givenName"=>"Peter", "familyName"=>"Slaughter", "@type"=>"Person", "@id"=>"https://orcid.org/0000-0002-2192-403X", "affiliation"=>{"@type"=>"Organization", "name"=>"NCEAS"}}, {"name"=>"University Of California, Santa Barbara", "@type"=>"Organization"}]) expect(json["version"]).to eq("2.0.0") expect(json["keywords"]).to eq("data sharing, data repository, DataONE") end it "Funding" do input = "https://doi.org/10.5438/6423" subject = Bolognese::Metadata.new(input: input) json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5438/6423") expect(json["@type"]).to eq("Collection") expect(json["hasPart"].length).to eq(25) expect(json["hasPart"].first).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5281/zenodo.30799") expect(json["funder"]).to eq("@id"=>"https://doi.org/10.13039/501100000780", "@type"=>"Organization", "name"=>"European Commission") expect(json["license"]).to eq("https://creativecommons.org/licenses/by/4.0/legalcode") end it "Funding OpenAIRE" do input = "https://doi.org/10.5281/ZENODO.1239" subject = Bolognese::Metadata.new(input: input) json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5281/zenodo.1239") expect(json["@type"]).to eq("Dataset") expect(json["funder"]).to eq("@id"=>"https://doi.org/10.13039/501100000780", "@type"=>"Organization", "name"=>"European Commission") expect(json["license"]).to eq(["https://creativecommons.org/publicdomain/zero/1.0/legalcode", "info:eu-repo/semantics/openAccess"]) end it "subject scheme" do input = "https://doi.org/10.4232/1.2745" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.4232/1.2745") expect(json["@type"]).to eq("Dataset") expect(json["name"]).to eq("Flash Eurobarometer 54 (Madrid Summit)") expect(json["keywords"]).to eq("KAT12 International Institutions, Relations, Conditions") end it "subject scheme multiple keywords" do input = "https://doi.org/10.1594/pangaea.721193" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.1594/pangaea.721193") expect(json["@type"]).to eq("Dataset") expect(json["name"]).to eq("Seawater carbonate chemistry and processes during experiments with Crassostrea gigas, 2007, supplement to: Kurihara, Haruko; Kato, Shoji; Ishimatsu, Atsushi (2007): Effects of increased seawater pCO2 on early development of the oyster Crassostrea gigas. Aquatic Biology, 1(1), 91-98") expect(json["keywords"]).to eq("Animalia, Bottles or small containers/Aquaria ( 20 L), Calcification/Dissolution, Coast and continental shelf, Crassostrea gigas, Development, Growth/Morphology, Laboratory experiment, Mollusca, North Pacific, Pelagos, Single species, Temperate, Zooplankton, Experimental treatment, Carbonate system computation flag, Temperature, water, Salinity, pH, Alkalinity, total, Carbon, inorganic, dissolved, Carbon dioxide, Bicarbonate ion, Carbonate ion, Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), Fugacity of carbon dioxide (water) at sea surface temperature (wet air), Aragonite saturation state, Calcite saturation state, Proportion, Crassostrea gigas, larvae length, Crassostrea gigas, larvae height, Crassostrea gigas, non mineralized, Crassostrea gigas, partially mineralized, Crassostrea gigas, fully mineralized, Calculated using seacarb after Nisumaa et al. (2010), Refractometer (Atago 100-S), pH meter (Mettler Toledo), pH meter (PHM290, Radiometer), Measured, European Project on Ocean Acidification (EPOCA), European network of excellence for Ocean Ecosystems Analysis (EUR-OCEANS), Ocean Acidification International Coordination Centre (OA-ICC)") expect(json["license"]).to eq("https://creativecommons.org/licenses/by/3.0/legalcode") end it "author is organization" do input = fixture_path + 'gtex.xml' url = "https://ors.datacite.org/doi:/10.25491/9hx8-ke93" content_url = "https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz" subject = Bolognese::Metadata.new(input: input, url: url, content_url: content_url, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.25491/9hx8-ke93") expect(json["@type"]).to eq("Dataset") expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium") expect(json["url"]).to eq("https://ors.datacite.org/doi:/10.25491/9hx8-ke93") expect(json["encodingFormat"]).to eq("application/tar") expect(json["contentSize"]).to eq("15.7M") expect(json["contentUrl"]).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz") expect(json["includedInDataCatalog"]).to eq("@id"=>"https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663", "@type"=>"DataCatalog", "name"=>"GTEx") expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1038/nmeth.4407", "@type"=>"ScholarlyArticle"}) end it "series information" do input = "10.4229/23RDEUPVSEC2008-5CO.8.3" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.4229/23rdeupvsec2008-5co.8.3") expect(json["@type"]).to eq("ScholarlyArticle") expect(json["name"]).to eq("Rural Electrification With Hybrid Power Systems Based on Renewables - Technical System Configurations From the Point of View of the European Industry") expect(json["author"].count).to eq(3) expect(json["author"].first).to eq("@type"=>"Person", "name"=>"P. Llamas", "givenName"=>"P.", "familyName"=>"Llamas") expect(json["periodical"]).to eq("@type"=>"Series", "firstPage"=>"Spain; 3353", "lastPage"=>"3356", "name"=>"23rd European Photovoltaic Solar Energy Conference and Exhibition", "volume"=>"1-5 September 2008") end it "data catalog" do input = "10.25491/8KMC-G314" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.25491/8kmc-g314") expect(json["@type"]).to eq("Dataset") expect(json["name"]).to eq("Covariates used in eQTL analysis. Includes genotyping principal components and PEER factors") expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium") expect(json["includedInDataCatalog"]).to eq("@type"=>"DataCatalog", "name"=>"GTEx") expect(json["identifier"]).to eq([{"@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.25491/8kmc-g314"},{"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"c7c89fe7366d50cd75448aa603c9de58"}]) expect(json["contentUrl"]).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_covariates.tar.gz") end it "alternate identifiers" do input = "10.23725/8na3-9s47" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.23725/8na3-9s47") expect(json["@type"]).to eq("Dataset") expect(json["name"]).to eq("NWD165827.recab.cram") expect(json["author"]).to eq("name"=>"TOPMed") expect(json["includedInDataCatalog"]).to be_nil expect(json["identifier"]).to eq( [{"@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.23725/8na3-9s47"}, {"@type"=>"PropertyValue", "propertyID"=>"minid", "value"=>"ark:/99999/fk41CrU4eszeLUDe"}, {"@type"=>"PropertyValue", "propertyID"=>"dataguid", "value"=>"dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7"}, {"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"3b33f6b9338fccab0901b7d317577ea3"}] ) expect(json["contentUrl"]).to include("s3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram", "gs://topmed-irc-share/public/NWD165827.recab.cram") end it "affiliation identifier" do input = fixture_path + 'datacite-example-affiliation.xml' subject = Bolognese::Metadata.new(input: input) json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5072/example-full") expect(json["@type"]).to eq("SoftwareSourceCode") expect(json["name"]).to eq("Full DataCite XML Example") expect(json["author"].length).to eq(3) expect(json["author"].first).to eq("@id" => "https://orcid.org/0000-0001-5000-0007", "@type" => "Person", "affiliation" => {"@id"=>"https://ror.org/04wxnsj81", "@type"=>"Organization", "name"=>"DataCite"}, "familyName" => "Miller", "givenName" => "Elizabeth", "name" => "Elizabeth Miller") expect(json["identifier"]).to eq( [{"@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.5072/example-full"}, {"@type"=>"PropertyValue", "propertyID"=>"URL", "value"=>"https://schema.datacite.org/meta/kernel-4.2/example/datacite-example-full-v4.2.xml"}] ) expect(json["license"]).to eq("https://creativecommons.org/publicdomain/zero/1.0/legalcode") end it "geo_location_point" do input = fixture_path + 'datacite-example-geolocation-2.xml' doi = "10.6071/Z7WC73" subject = Bolognese::Metadata.new(input: input, doi: doi) json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.6071/z7wc73") expect(json["@type"]).to eq("Dataset") expect(json["name"]).to eq("Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek meteorological data, soil moisture and temperature, snow depth and air temperature") expect(json["author"].length).to eq(6) expect(json["author"][2]).to eq("@id"=>"https://orcid.org/0000-0002-8862-1404", "@type"=>"Person", "familyName"=>"Stacy", "givenName"=>"Erin", "name"=>"Erin Stacy", "affiliation" => {"@type"=>"Organization", "name"=>"UC Merced"}) expect(json["includedInDataCatalog"]).to be_nil expect(json["spatialCoverage"]).to eq([{"@type"=>"Place", "geo"=> {"@type"=>"GeoCoordinates", "address"=>"Providence Creek (Lower, Upper and P301)", "latitude"=>"37.047756", "longitude"=>"-119.221094"}}, {"@type"=>"Place", "geo"=> {"@type"=>"GeoShape", "address"=>"Providence Creek (Lower, Upper and P301)", "box"=>"37.046 -119.211 37.075 -119.182"}}]) expect(json["license"]).to eq("https://creativecommons.org/licenses/by/4.0/legalcode") end it "geo_location_box" do input = "10.1594/PANGAEA.842237" subject = Bolognese::Metadata.new(input: input, from: "datacite") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.1594/pangaea.842237") expect(json["@type"]).to eq("Dataset") expect(json["name"]).to eq("Registry of all stations from the Tara Oceans Expedition (2009-2013)") expect(json["author"]).to eq([{"familyName"=>"Tara Oceans Consortium", "givenName"=>"Coordinators", "name"=>"Coordinators Tara Oceans Consortium"}, {"familyName"=>"Tara Oceans Expedition", "givenName"=>"Participants", "name"=>"Participants Tara Oceans Expedition"}]) expect(json["includedInDataCatalog"]).to be_nil expect(json["identifier"]).to eq("@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.1594/pangaea.842237") expect(json["spatialCoverage"]).to eq("@type"=>"Place", "geo"=>{"@type"=>"GeoShape", "box"=>"-64.3088 -168.5182 79.6753 174.9006"}) expect(json["license"]).to eq("https://creativecommons.org/licenses/by/3.0/legalcode") end it "geo_location_polygon" do input = fixture_path + 'datacite-example-polygon-v4.1.xml' subject = Bolognese::Metadata.new(input: input) json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.5072/example-polygon") expect(json["@type"]).to eq("Dataset") expect(json["name"]).to eq("Meteo measurements at the Sand Motor") expect(json["author"]).to eq("@type"=>"Person", "familyName"=>"Den Heijer", "givenName"=>"C", "name"=>"C Den Heijer") expect(json["includedInDataCatalog"]).to be_nil expect(json["identifier"]).to eq("@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.5072/example-polygon") expect(json["spatialCoverage"].dig("geo", "polygon").length).to eq(34) expect(json["spatialCoverage"].dig("geo", "polygon").first).to eq(["4.1738852605822", "52.03913926329928"]) end it "from schema_org gtex" do input = fixture_path + 'schema_org_gtex.json' subject = Bolognese::Metadata.new(input: input, from: "schema_org") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.25491/d50j-3083") expect(json["@type"]).to eq("Dataset") expect(json["identifier"]).to eq([{"@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.25491/d50j-3083"}, {"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"687610993"}]) expect(json["url"]).to eq("https://ors.datacite.org/doi:/10.25491/d50j-3083") expect(json["additionalType"]).to eq("Gene expression matrices") expect(json["name"]).to eq("Fully processed, filtered and normalized gene expression matrices (in BED format) for each tissue, which were used as input into FastQTL for eQTL discovery") expect(json["version"]).to eq("v7") expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium") expect(json["keywords"]).to eq("gtex, annotation, phenotype, gene regulation, transcriptomics") expect(json["datePublished"]).to eq("2017") expect(json["contentUrl"]).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz") expect(json["schemaVersion"]).to eq("http://datacite.org/schema/kernel-4") expect(json["includedInDataCatalog"]).to eq("@type"=>"DataCatalog", "name"=>"GTEx") expect(json["publisher"]).to eq("@type"=>"Organization", "name"=>"GTEx") expect(json["funder"]).to eq([{"@id"=>"https://doi.org/10.13039/100000052", "name"=>"Common Fund of the Office of the Director of the NIH", "@type"=>"Organization"}, {"@id"=>"https://doi.org/10.13039/100000054", "name"=>"National Cancer Institute (NCI)", "@type"=>"Organization"}, {"@id"=>"https://doi.org/10.13039/100000051", "name"=>"National Human Genome Research Institute (NHGRI)", "@type"=>"Organization"}, {"@id"=>"https://doi.org/10.13039/100000050", "name"=>"National Heart, Lung, and Blood Institute (NHLBI)", "@type"=>"Organization"}, {"@id"=>"https://doi.org/10.13039/100000026", "name"=>"National Institute on Drug Abuse (NIDA)", "@type"=>"Organization"}, {"@id"=>"https://doi.org/10.13039/100000025", "name"=>"National Institute of Mental Health (NIMH)", "@type"=>"Organization"}, {"@id"=>"https://doi.org/10.13039/100000065", "name"=>"National Institute of Neurological Disorders and Stroke (NINDS)", "@type"=>"Organization"}]) expect(json["provider"]).to eq("@type"=>"Organization", "name"=>"DataCite") end it "from schema_org topmed" do input = fixture_path + 'schema_org_topmed.json' subject = Bolognese::Metadata.new(input: input, from: "schema_org") json = JSON.parse(subject.schema_org) expect(json["@id"]).to eq("https://doi.org/10.23725/8na3-9s47") expect(json["@type"]).to eq("Dataset") expect(json["identifier"]).to eq( [{"@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.23725/8na3-9s47"}, {"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"3b33f6b9338fccab0901b7d317577ea3"}, {"@type"=>"PropertyValue", "propertyID"=>"minid", "value"=>"ark:/99999/fk41CrU4eszeLUDe"}, {"@type"=>"PropertyValue", "propertyID"=>"dataguid", "value"=>"dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7"}]) expect(json["url"]).to eq("https://ors.datacite.org/doi:/10.23725/8na3-9s47") expect(json["additionalType"]).to eq("CRAM file") expect(json["name"]).to eq("NWD165827.recab.cram") expect(json["author"]).to eq("@type"=>"Organization", "name"=>"TOPMed IRC") expect(json["keywords"]).to eq("topmed, whole genome sequencing") expect(json["datePublished"]).to eq("2017-11-30") expect(json["contentUrl"]).to eq(["s3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram", "gs://topmed-irc-share/public/NWD165827.recab.cram"]) expect(json["schemaVersion"]).to eq("http://datacite.org/schema/kernel-4") expect(json["publisher"]).to eq("@type"=>"Organization", "name"=>"TOPMed") expect(json["citation"]).to eq("@id"=>"https://doi.org/10.23725/2g4s-qv04", "@type"=>"Dataset") expect(json["funder"]).to eq("@id"=>"https://doi.org/10.13039/100000050", "@type"=>"Organization", "name"=>"National Heart, Lung, and Blood Institute (NHLBI)") expect(json["provider"]).to eq("@type"=>"Organization", "name"=>"DataCite") end end end